Characterization and exploitation of plasmids controlling naphthalene biodegradation by Pseudomonas species

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Objectif

This project addresses an important environmental problem affecting all of Europe - namely, the mechanisms for dealing with land contaminated with polycyclic aromatic hydrocarbons (PAHs), which create major health problems. Bioremediation of such pollution has some advantages in that it should not involve removal of the material to a new site, but bioremediation is slow and is often impractical when a prime site is needed for development on a short time frame. Therefore the more that is understood about the process of bioremediation the more likely it is that we can harness the natural ability of micro-organisms to return a site to a safe and healthy place to live and work. We have chosen the degradation of naphthalene as our model system since this compound is a major component of many contaminated sites, and it is relatively straightforward to isolate bacteria that carry genes promoting the degradation. These genes are often carried on large mobile genetic elements called plasmids. The interaction between the plasmid and its host can affect both the stability of the host-plasmid combination and the ability of the host to associate productively with the rhizosphere of the plants growing in the contaminated soil. Therefore we wish to study the relationships of the naphthalene-degrading genes to the plasmids that carry them, the relationship between the mobile elements and the host and the relationships between the host and the plants that can provide the most productive part of the soil/plant environment.

The programme involves collaboration between experts on bacterial bioremediation, the genetics of mobile elements in bacteria, the genetic dissection and replication of the mobile elements, and soil ecology including the relationships to plants. The programme starts with a survey of the diversity of useful systems. It will employ genomic approaches, including the complete DNA sequence of at least one mobile element carrying genes for naphthalene degradation and array technology with genes room the whole element. This will provide a thorough molecular description of the structure, activity and distribution of elements of the same sort in polluted sites in both Russia and Belarus. Through molecular approaches it will attempt to identify the ways that such elements interact with each other and how they evolve to provide more effective pathways for degradation. Studies in soil microcosms will investigate the influence of soil conditions on expression of the biodegradation genes as well as determining which plasmid-host combination works most effectively. The spread of the plasmids to indigenous bacteria will be followed through the use of molecular probes. Finally model plant-soil systems will be studied to determine the effect of this extra dimension.

The outcome from this work will be a catalogue of useful plasmids, and details of the conditions under which the properties that they confer are optimised in relation to host bacterium as well as soil and rhizosphere environment. This may lead to a demonstration project in which field trials of specific gene-microbe-plant combinations can be tested in specific soils for optimised bioremediation and combined with culture conditions, which will promote the most rapid evolution of an active degradative community.